plot_similarity: The position of the nodes is based on the similarity between...

In llrs/BioCor: Functional similarities

The position of the nodes is based on the similarity between them.

Description

The position of the nodes is based on the similarity between them.

Plot how similar are the data

Usage

plot_data(x, top)

plot_similarity(pd)

Arguments

x	Matrix with the similarities.
top	a number between 0 and 1 to select the edges relating the elements of the matrix.
pd	The plot data from plot_data() function.

Value

A list with two elements:

• nodes: The position and name of the nodes

• edges: The information about the selected edges

A ggplot object

Examples

if (require("org.Hs.eg.db") & require("reactome.db")) {
  # Extract the paths of all genes of org.Hs.eg.db from KEGG
  # (last update in data of June 31st 2011)
  genes.kegg <- as.list(org.Hs.egPATH)
  # Extracts the paths of all genes of org.Hs.eg.db from reactome
  genes.react <- as.list(reactomeEXTID2PATHID)

  sim <- mgeneSim(c("81", "18", "10"), genes.react)
  pd <- plot_data(sim, top = 0.25)
  if (requireNamespace("ggplot2", quietly = TRUE)){
    plot_similarity(pd)
  }
}

llrs/BioCor documentation built on April 24, 2024, 5:50 p.m.